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Fusion Protein:KDM5B-PPP1R12B |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: KDM5B-PPP1R12B | FusionPDB ID: 41865 | FusionGDB2.0 ID: 41865 | Hgene | Tgene | Gene symbol | KDM5B | PPP1R12B | Gene ID | 10765 | 4660 |
Gene name | lysine demethylase 5B | protein phosphatase 1 regulatory subunit 12B | |
Synonyms | CT31|JARID1B|MRT65|PLU-1|PLU1|PPP1R98|PUT1|RBBP2H1A|RBP2-H1 | MYPT2|PP1bp55 | |
Cytomap | 1q32.1 | 1q32.1 | |
Type of gene | protein-coding | protein-coding | |
Description | lysine-specific demethylase 5Bcancer/testis antigen 31histone demethylase JARID1Bjumonji, AT rich interactive domain 1Bjumonji/ARID domain-containing protein 1Blysine (K)-specific demethylase 5Bprotein phosphatase 1, regulatory subunit 98putative D | protein phosphatase 1 regulatory subunit 12Bmyosin phosphatase target subunit 2myosin phosphatase-targeting subunit 2protein phosphatase 1, regulatory (inhibitor) subunit 12B | |
Modification date | 20200320 | 20200313 | |
UniProtAcc | Q9UGL1 Main function of 5'-partner protein: FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5 (PubMed:24952722). In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250|UniProtKB:Q80Y84, ECO:0000269|PubMed:12657635, ECO:0000269|PubMed:16645588, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17363312, ECO:0000269|PubMed:24952722, ECO:0000269|PubMed:26645689, ECO:0000269|PubMed:26741168, ECO:0000269|PubMed:27214403, ECO:0000269|PubMed:28262558}. | . | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000367264, ENST00000367265, ENST00000456180, | ENST00000290419, ENST00000367270, ENST00000391959, ENST00000356764, ENST00000480184, ENST00000336894, ENST00000608999, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 14 X 13 X 9=1638 | 14 X 15 X 6=1260 |
# samples | 17 | 16 | |
** MAII score | log2(17/1638*10)=-3.26832870550331 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(16/1260*10)=-2.97727992349992 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: KDM5B [Title/Abstract] AND PPP1R12B [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: KDM5B [Title/Abstract] AND PPP1R12B [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | KDM5B(202742246)-PPP1R12B(202536906), # samples:2 | ||
Anticipated loss of major functional domain due to fusion event. | KDM5B-PPP1R12B seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. KDM5B-PPP1R12B seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. KDM5B-PPP1R12B seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. KDM5B-PPP1R12B seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
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Partner | Gene | GO ID | GO term | PubMed ID |
Hgene | KDM5B | GO:0034720 | histone H3-K4 demethylation | 20228790 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:202742246/chr1:202536906) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Amino Acid Sequences |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
ENST00000367265 | KDM5B | chr1 | 202742246 | - | ENST00000608999 | PPP1R12B | chr1 | 202536906 | + | 14079 | 1741 | 934 | 1932 | 332 |
ENST00000367265 | KDM5B | chr1 | 202742246 | - | ENST00000336894 | PPP1R12B | chr1 | 202536906 | + | 9942 | 1741 | 934 | 1932 | 332 |
ENST00000367264 | KDM5B | chr1 | 202742246 | - | ENST00000608999 | PPP1R12B | chr1 | 202536906 | + | 13027 | 689 | 113 | 880 | 255 |
ENST00000367264 | KDM5B | chr1 | 202742246 | - | ENST00000336894 | PPP1R12B | chr1 | 202536906 | + | 8890 | 689 | 113 | 880 | 255 |
ENST00000367265 | KDM5B | chr1 | 202743740 | - | ENST00000608999 | PPP1R12B | chr1 | 202385914 | + | 16374 | 1570 | 934 | 4227 | 1097 |
ENST00000367265 | KDM5B | chr1 | 202743740 | - | ENST00000336894 | PPP1R12B | chr1 | 202385914 | + | 12237 | 1570 | 934 | 4227 | 1097 |
ENST00000367265 | KDM5B | chr1 | 202743740 | - | ENST00000480184 | PPP1R12B | chr1 | 202385914 | + | 2955 | 1570 | 934 | 2826 | 630 |
ENST00000367265 | KDM5B | chr1 | 202743740 | - | ENST00000356764 | PPP1R12B | chr1 | 202385914 | + | 2842 | 1570 | 934 | 2439 | 501 |
ENST00000367264 | KDM5B | chr1 | 202743740 | - | ENST00000608999 | PPP1R12B | chr1 | 202385914 | + | 15322 | 518 | 113 | 3175 | 1020 |
ENST00000367264 | KDM5B | chr1 | 202743740 | - | ENST00000336894 | PPP1R12B | chr1 | 202385914 | + | 11185 | 518 | 113 | 3175 | 1020 |
ENST00000367264 | KDM5B | chr1 | 202743740 | - | ENST00000480184 | PPP1R12B | chr1 | 202385914 | + | 1903 | 518 | 113 | 1774 | 553 |
ENST00000367264 | KDM5B | chr1 | 202743740 | - | ENST00000356764 | PPP1R12B | chr1 | 202385914 | + | 1790 | 518 | 113 | 1387 | 424 |
ENST00000367265 | KDM5B | chr1 | 202743741 | - | ENST00000608999 | PPP1R12B | chr1 | 202385915 | + | 16374 | 1570 | 934 | 4227 | 1097 |
ENST00000367265 | KDM5B | chr1 | 202743741 | - | ENST00000336894 | PPP1R12B | chr1 | 202385915 | + | 12237 | 1570 | 934 | 4227 | 1097 |
ENST00000367265 | KDM5B | chr1 | 202743741 | - | ENST00000480184 | PPP1R12B | chr1 | 202385915 | + | 2955 | 1570 | 934 | 2826 | 630 |
ENST00000367265 | KDM5B | chr1 | 202743741 | - | ENST00000356764 | PPP1R12B | chr1 | 202385915 | + | 2842 | 1570 | 934 | 2439 | 501 |
ENST00000367264 | KDM5B | chr1 | 202743741 | - | ENST00000608999 | PPP1R12B | chr1 | 202385915 | + | 15322 | 518 | 113 | 3175 | 1020 |
ENST00000367264 | KDM5B | chr1 | 202743741 | - | ENST00000336894 | PPP1R12B | chr1 | 202385915 | + | 11185 | 518 | 113 | 3175 | 1020 |
ENST00000367264 | KDM5B | chr1 | 202743741 | - | ENST00000480184 | PPP1R12B | chr1 | 202385915 | + | 1903 | 518 | 113 | 1774 | 553 |
ENST00000367264 | KDM5B | chr1 | 202743741 | - | ENST00000356764 | PPP1R12B | chr1 | 202385915 | + | 1790 | 518 | 113 | 1387 | 424 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000367265 | ENST00000608999 | KDM5B | chr1 | 202742246 | - | PPP1R12B | chr1 | 202536906 | + | 0.025801014 | 0.97419894 |
ENST00000367265 | ENST00000336894 | KDM5B | chr1 | 202742246 | - | PPP1R12B | chr1 | 202536906 | + | 0.016986378 | 0.98301363 |
ENST00000367264 | ENST00000608999 | KDM5B | chr1 | 202742246 | - | PPP1R12B | chr1 | 202536906 | + | 0.002909706 | 0.9970902 |
ENST00000367264 | ENST00000336894 | KDM5B | chr1 | 202742246 | - | PPP1R12B | chr1 | 202536906 | + | 0.002251573 | 0.99774843 |
ENST00000367265 | ENST00000608999 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.001191681 | 0.9988084 |
ENST00000367265 | ENST00000336894 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.000993151 | 0.9990069 |
ENST00000367265 | ENST00000480184 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.003393066 | 0.99660695 |
ENST00000367265 | ENST00000356764 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.00214105 | 0.99785894 |
ENST00000367264 | ENST00000608999 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.00053345 | 0.9994666 |
ENST00000367264 | ENST00000336894 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.000443036 | 0.99955696 |
ENST00000367264 | ENST00000480184 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.003725199 | 0.9962748 |
ENST00000367264 | ENST00000356764 | KDM5B | chr1 | 202743740 | - | PPP1R12B | chr1 | 202385914 | + | 0.001472818 | 0.99852717 |
ENST00000367265 | ENST00000608999 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.001191681 | 0.9988084 |
ENST00000367265 | ENST00000336894 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.000993151 | 0.9990069 |
ENST00000367265 | ENST00000480184 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.003393066 | 0.99660695 |
ENST00000367265 | ENST00000356764 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.00214105 | 0.99785894 |
ENST00000367264 | ENST00000608999 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.00053345 | 0.9994666 |
ENST00000367264 | ENST00000336894 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.000443036 | 0.99955696 |
ENST00000367264 | ENST00000480184 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.003725199 | 0.9962748 |
ENST00000367264 | ENST00000356764 | KDM5B | chr1 | 202743741 | - | PPP1R12B | chr1 | 202385915 | + | 0.001472818 | 0.99852717 |
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Get the fusion protein sequences from here. |
Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for KDM5B-PPP1R12B |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
KDM5B | chr1 | 202742246 | PPP1R12B | chr1 | 202536906 | 1741 | 263 | HYERILNPYNLFLSGDSLRQKQEKTS |
KDM5B | chr1 | 202742246 | PPP1R12B | chr1 | 202536906 | 689 | 186 | HYERILNPYNLFLSGDSLRQKQEKTS |
KDM5B | chr1 | 202743740 | PPP1R12B | chr1 | 202385914 | 1570 | 212 | VERKILDLFQLNKACIDENLDMVKFL |
KDM5B | chr1 | 202743740 | PPP1R12B | chr1 | 202385914 | 518 | 135 | VERKILDLFQLNKACIDENLDMVKFL |
KDM5B | chr1 | 202743741 | PPP1R12B | chr1 | 202385915 | 1570 | 212 | VERKILDLFQLNKACIDENLDMVKFL |
KDM5B | chr1 | 202743741 | PPP1R12B | chr1 | 202385915 | 518 | 135 | VERKILDLFQLNKACIDENLDMVKFL |
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Potential FusionNeoAntigen Information of KDM5B-PPP1R12B in HLA I |
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KDM5B-PPP1R12B_202742246_202536906.msa |
![]() * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
KDM5B-PPP1R12B | chr1 | 202742246 | chr1 | 202536906 | 689 | HLA-B15:30 | NLFLSGDSL | 0.5941 | 0.7307 | 9 | 18 |
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Potential FusionNeoAntigen Information of KDM5B-PPP1R12B in HLA II |
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![]() * We used NetMHCIIpan v4.1 (%rank<0.5). |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of KDM5B-PPP1R12B |
![]() * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
6332 | NPYNLFLSGDSLRQ | KDM5B | PPP1R12B | chr1 | 202742246 | chr1 | 202536906 | 689 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KDM5B-PPP1R12B |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
HLA-B14:02 | 3BVN | 6332 | NPYNLFLSGDSLRQ | -7.9962 | -8.1096 |
HLA-B14:02 | 3BVN | 6332 | NPYNLFLSGDSLRQ | -5.70842 | -6.74372 |
HLA-B52:01 | 3W39 | 6332 | NPYNLFLSGDSLRQ | -6.83737 | -6.95077 |
HLA-B52:01 | 3W39 | 6332 | NPYNLFLSGDSLRQ | -4.4836 | -5.5189 |
HLA-A11:01 | 4UQ2 | 6332 | NPYNLFLSGDSLRQ | -10.0067 | -10.1201 |
HLA-A11:01 | 4UQ2 | 6332 | NPYNLFLSGDSLRQ | -9.03915 | -10.0745 |
HLA-A24:02 | 5HGA | 6332 | NPYNLFLSGDSLRQ | -6.56204 | -6.67544 |
HLA-A24:02 | 5HGA | 6332 | NPYNLFLSGDSLRQ | -5.42271 | -6.45801 |
HLA-B44:05 | 3DX8 | 6332 | NPYNLFLSGDSLRQ | -7.85648 | -8.89178 |
HLA-B44:05 | 3DX8 | 6332 | NPYNLFLSGDSLRQ | -5.3978 | -5.5112 |
HLA-A02:01 | 6TDR | 6332 | NPYNLFLSGDSLRQ | -3.37154 | -4.40684 |
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Vaccine Design for the FusionNeoAntigens of KDM5B-PPP1R12B |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
KDM5B-PPP1R12B | chr1 | 202742246 | chr1 | 202536906 | 9 | 18 | NLFLSGDSL | GACAGCCTAAGGCAGAAACAAGAAAAG |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of KDM5B-PPP1R12B |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
SARC | KDM5B-PPP1R12B | chr1 | 202742246 | ENST00000367264 | chr1 | 202536906 | ENST00000336894 | TCGA-DX-A8BV-01A |
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Potential target of CAR-T therapy development for KDM5B-PPP1R12B |
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![]() * Minus value of BPloci means that the break point is located before the CDS. |
- In-frame and retained 'Transmembrane'. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
![]() * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to KDM5B-PPP1R12B |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to KDM5B-PPP1R12B |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |